Query Result Differences

I have a fairly big query (LINQ), and when I run it in LINQPad, I get 90,189 records in my result set. Copying the LINQ statement to a C# app, and running the same LINQ statement results in 87,776 records. Why would there be a difference in the number of records returned?

The only difference between the two is the LINQPad is using LINQPads data context and entity model, and the C# app is using EntityFrameworks, but the underlying data should still be the same, no?

Also, 1 other changes was necessary; I had to remove a call to IndexOf, and replace it with SqlFunctions.CharIndex() call.